Personal information

Keywords

Biocondutor, Software Development, Data Management

Countries

Germany

Activities

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Employment (4)

European Molecular Biology Laboratory: Heidelberg, DE

2023-05-15 to present | Data Management Coordinator (Data Science Centre)
Employment
Source: Self-asserted source
Mike L. Smith

European Molecular Biology Organization: Heidelberg, DE

2018-02 to 2023-05-14 | Senior Scientific Programmer
Employment
Source: Self-asserted source
Mike L. Smith

European Molecular Biology Laboratory: Heidelberg, DE

2015-11 to 2018-02 | Bioinformatician
Employment
Source: Self-asserted source
Mike L. Smith

University of Cambridge: Cambridge, GB

2013-01 to 2015-10 | Research Associate (CRUK CI)
Employment
Source: Self-asserted source
Mike L. Smith

Education and qualifications (3)

University of Cambridge: Cambridge, Cambridgeshire, GB

2009-01 to 2013-01 | PhD (Oncology)
Education
Source: Self-asserted source
Mike L. Smith

Cardiff University: Cardiff, Cardiff, GB

2007-09 to 2008-09 | MSc in Bioinformatics (Medicine)
Education
Source: Self-asserted source
Mike L. Smith

University of Bath: Bath, Bath and North East Somer, GB

2003-10 to 2007-07 | BSc in Mathematics and Computing (Mathematics)
Education
Source: Self-asserted source
Mike L. Smith

Works (18)

PCR Duplicate Proportion Estimation and Consequences for DNA Copy Number Calculations

2022 | Book chapter
DOI: 10.1007/978-3-031-12766-3_18
Contributors: Andy G. Lynch; Mike L. Smith; Matthew D. Eldridge; Simon Tavaré
Source: check_circle
Crossref

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Nature Protocols
2021-12 | Journal article
DOI: 10.1038/s41596-021-00630-1
Contributors: Rozemarijn W. D. Kleinendorst; Guido Barzaghi; Mike L. Smith; Judith B. Zaugg; Arnaud R. Krebs
Source: check_circle
Crossref

Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells

Cell Reports
2020-04-07 | Journal article
DOI: 10.1016/j.celrep.2020.03.029
Part of ISSN: 2211-1247
Source: Self-asserted source
Mike L. Smith

Orchestrating single-cell analysis with Bioconductor.

Nature methods
2019-12 | Journal article
DOI: 10.1038/s41592-019-0654-x
PMID: 31792435
PMC: PMC7358058
Contributors: Amezquita RA; Lun ATL; Becht E; Carey VJ; Carpp LN; Geistlinger L; Marini F; Rue-Albrecht K; Risso D; Soneson C et al.
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

Transcriptomic profiling reveals three molecular phenotypes of adenocarcinoma at the gastroesophageal junction

International Journal of Cancer
2019-12-15 | Journal article
DOI: 10.1002/ijc.32384
Part of ISSN: 0020-7136
Part of ISSN: 1097-0215
Source: Self-asserted source
Mike L. Smith

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types

PLOS Computational Biology
2018-05-03 | Journal article
DOI: 10.1371/journal.pcbi.1006135
DOI: 10.1101/167445
Contributors: Aaron T. L. Lun; Mihaela Pertea; Hervé Pagès; Mike L. Smith
Source: Self-asserted source
Mike L. Smith
grade
Preferred source (of 3)‎

Authoring Bioconductor workflows with BiocWorkflowTools [version 1; referees: awaiting peer review]

2018-04-06 | Journal article
DOI: 10.12688/f1000research.14399.1
Part of ISSN: 2046-1402
Contributors: Mike L. Smith; Andrzej K. Oleś; Wolfgang Huber
Source: check_circle
F1000
grade
Preferred source (of 2)‎

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data

2017-05-19 | Preprint
DOI: 10.1101/139972
Contributors: James HR Farmery; Mike L Smith; Andy G Lynch
Source: check_circle
Crossref

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

2014-08 | Journal article
DOI: 10.1038/ng.3013
PMID: 24952744
PMC: PMC4116294
Contributors: Weaver JM; Ross-Innes CS; Shannon N; Lynch AG; Forshew T; Barbera M; Murtaza M; Ong CA; Lao-Sirieix P; Dunning MJ et al.
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

illuminaio: An open source IDAT parsing tool for Illumina microarrays.

2013 | Journal article
DOI: 10.12688/f1000research.2-264.v1
PMID: 24701342
PMC: PMC3968891
Contributors: Smith ML; Baggerly KA; Bengtsson H; Ritchie ME; Hansen KD
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

BeadArray expression analysis using bioconductor.

2011-12 | Journal article
DOI: 10.1371/journal.pcbi.1002276
PMID: 22144879
PMC: PMC3228778
Contributors: Ritchie ME; Dunning MJ; Smith ML; Shi W; Lynch AG
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

BayesPeak--an R package for analysing ChIP-seq data.

2011-03 | Journal article
DOI: 10.1093/bioinformatics/btq685
PMID: 21245054
PMC: PMC3042177
Contributors: Cairns J; Spyrou C; Stark R; Smith ML; Lynch AG; Tavaré S
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

Genetic differences between five European populations.

2010 | Journal article
DOI: 10.1159/000313854
PMID: 20616560
Contributors: Moskvina V; Smith M; Ivanov D; Blackwood D; StClair D; Hultman C; Toncheva D; Gill M; Corvin A; O'Dushlaine C et al.
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data.

2010 | Journal article
DOI: 10.1186/1471-2105-11-208
PMID: 20423502
PMC: PMC2880029
Contributors: Smith ML; Dunning MJ; Tavaré S; Lynch AG
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies.

2010-09 | Journal article
PMID: 20981138
PMC: PMC2956622
Contributors: Smith ML; Lynch AG
Source: Self-asserted source
Mike L. Smith via Europe PubMed Central

beadarray: R classes and methods for Illumina bead-based data

Bioinformatics
2007-08-15 | Journal article
DOI: 10.1093/bioinformatics/btm311
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Contributors: M. J. Dunning; Mike L. Smith; M. E. Ritchie; S. Tavare
Source: Self-asserted source
Mike L. Smith

Quality Control and Low-Level Statistical Analysis of Illumina BeadArray

REVSTAT-Statistical Journal
2006-03-30 | Journal article
DOI: 10.57805/REVSTAT.V4I1.24
Contributors: Mark J. Dunning; Natalie P. Thorne; Isabelle Camilier; Mike L. Smith; Simon Tavaré
Source: Self-asserted source
Mike L. Smith

Rarr

Bioconductor
Software | Conceptualization, Software
DOI: 10.18129/B9.bioc.Rarr
Contributors: Mike L. Smith
Source: Self-asserted source
Mike L. Smith

Peer review (1 review for 1 publication/grant)

Review activity for F1000Research. (1)
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